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1,243 results for “Statistics”
Combining statistical and mechanistic models to unravel the drivers of mortality within a rear-edge beech population - Supporting Material
<p>Supporting material for the study:</p> <p><strong>"Combining statistical and mechanistic models to unravel the drivers of mortality within a rear-edge beech population."</strong></p> <p><strong>Authors:</strong></p> <p>Cathleen Petit-Cailleux1, Hendrik Davi1, François Lefèvre1, Joseph Garrigue<strong>2</strong>, Jean-André Magdalou<strong>2</strong>, Christophe Hurson<strong>2,3</strong><strong>, </strong>Elodie Magnanou<strong>2,4</strong>, and Sylvie Oddou-Muratorio1.</p> <p> </p> <p>Adresses</p> <p>1INRA, UR 629 Ecologie des Forêts Méditerranéennes, URFM, Avignon, France</p> <p><strong>2</strong>Réserve Naturelle Nationale de la Forêt de la Massane, France</p> <p><strong>3</strong>Fédération des Réserves Naturelles Catalanes, Prades, France</p> <p><strong>4</strong>Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France</p> <p><strong>ORCID:</strong></p> <p>Cathleen Petit-Cailleux: <a href="https://orcid.org/0000-0001-7714-6583">https://orcid.org/0000-0001-7714-6583</a></p> <p>François Lefèvre : <a href="https://orcid.org/0000-0003-2242-7251">https://orcid.org/0000-0003-2242-7251</a></p> <p>Sylvie Oddou-Muratorio <a href="https://orcid.org/0000-0003-2374-8313">https://orcid.org/0000-0003-2374-8313</a></p> <p> </p> <p>-------------</p> <p>Raw data of the Table_Massane_moratlity_trees.csv and climate can be obtained from Joseph Garrigue, Jean-André Magdalou and Christophe Hurson.</p> <p>The inventories files and daily climate are the input dataset to run CASTANEA models.</p> <p>All details are provided in the article.</p>
MetaboScope: A statistical toolbox for analyzing 1H nuclear magnetic resonance spectra from human clinical studies.
<p>MetaboScope is purposefully built as a pipeline where each module accepts the output generated by the previous one. This provides flexibility and simplicity of use, while being straightforward to maintain. The system and its libraries were developed in JavaScript and run as a web app; therefore, all the operations are performed on the local computer, circumventing the need to upload data. The code is open source (DOI: https://www.cheminfo.org/flavor/metabolomics/index.html) and can be readily installed locally. We provide module notes and video tutorials, in addition to clinical spectral datasets for modelling purposes.</p> <p>View data:</p> <p><a title="nmrium.org" href="https://www.nmrium.org/nmrium#?toc=https://zenodo.org/api/records/12916741/files/toc.json/content" target="_blank" rel="noopener">https://www.nmrium.org/nmrium#?toc=https://zenodo.org/api/records/12916741/files/toc.json/content</a></p>
Zonal Statistics of Weather Indicators for Brazilian Municipalities from the BR-DWGD Project
<p>This dataset presents daily weather indicators for Brazilian municipalities computed with zonal statistics using the data from the <a href="https://sites.google.com/site/alexandrecandidoxavierufes/brazilian-daily-weather-gridded-data" target="_blank" rel="noopener">BR-DWGD project</a> (version 3.2.3), from 1961-01-01 to 2024-03-20.</p> <p> </p> <table> <tbody> <tr> <td>File</td> <td>Indicator</td> <td>Unit</td> </tr> <tr> <td>pr_3.2.3.parquet</td> <td>Precipitation</td> <td>mm</td> </tr> <tr> <td>ETo_3.2.3.parquet</td> <td>Evapotranspiration</td> <td>mm</td> </tr> <tr> <td>Tmax_3.2.3.parquet</td> <td>Maximum temperature</td> <td>°C</td> </tr> <tr> <td>Tmin_3.2.3.parquet</td> <td>Minimum temperature</td> <td>°C</td> </tr> <tr> <td>Rs_3.2.3.parquet</td> <td>Solar radiation</td> <td>MJm-2</td> </tr> <tr> <td>u2_3.2.3.parquet</td> <td>Wind speed at 2 m height</td> <td>m/s</td> </tr> <tr> <td>RH_3.2.3.parquet</td> <td>Relative humidity</td> <td>%</td> </tr> </tbody> </table> <p>The methodology to compute the zonal statistics follows <a href="https://doi.org/10.1017/eds.2024.3" target="_blank" rel="noopener">https://doi.org/10.1017/eds.2024.3</a> .</p>
Data and statistical code for "Reconciling biodiversity with timber production and revenue via an intensive forest management experiment"
<p><strong>Abstract</strong></p> <p>Understanding how land-management intensification shapes the relationships between biodiversity, yield and economic benefit is critical for managing natural resources. Yet, manipulative experiments that test how herbicides affect these relationships are scarce, particularly in forest ecosystems where considerable time lags exist between harvest revenue and initial investments. We assessed these relationships by combining 7 years of biodiversity surveys (>800 taxa) and forecasts of timber yield and economic return from a replicated, large-scale experiment that manipulated herbicide application intensity in operational timber plantations. Herbicides reduced species richness across trophic groups (-18%), but responses by higher-level trophic groups were more variable (0–38% reduction) than plant responses (-40%). Financial discounting, a conventional economic method to standardize past and future cashflows, strongly modified biodiversity-revenue relationships caused by management intensity. Despite a projected 28% timber yield gain with herbicides, biodiversity-revenue tradeoffs were muted when opportunity costs were high (i.e., economic discount rates ≥7%). Although herbicides can drive biodiversity-yield tradeoffs, under certain conditions, financial discounting provides opportunities to reconcile biodiversity conservation with revenue.</p>
Dataset for statistical analysis of Constrictotermes cyphergaster (Blattodea: Isoptera: Termitidae: Nasutitermitinae) termites behavioural patterns
<p>This statistical analysis corresponds to the behavioral perspective of a large experiment in which <em>Constrictotermes cyphergaster</em> (Blattodea: Isoptera: Termitidae: Nasutitermitinae) termite groups were submitted to four different alarm stimuli. The aim of the work was to known the effect, at the individual scale, of the intensity of alarm stimuli in the emergence of order/disorder in group responses of social groups.</p> <p>The “read-me” file contains a detailed description of each data table used for the analysis. In the data tables, columns correspond to variables and rows to observations. Explanation of variables is on the headers of each data table.</p>
Dataset for statistical analysis of the habituation between the nest builder Cornitermes cumulans termites and their inquiline Curvitermes cf. odontognathus
<p>Here we present the dataset used for statistical analysis of the work aiming to known if habituation could attenuate host-inquiline lethal interactions, which could favor cohabitation in termites. For that, we tested the effect of the prior heterospecific exposure time on the behaviour and survival of termite hosts and inquilines during an encounter. We used as a biological model the nest builder termites <em>Cornitermes cumulans</em> and their inquiline <em>Curvitermes</em> cf. o<em>dontognathus</em>. We used prior heterospecific exposure times of 0, 60, 120, and 180 min where inquilines and builders were kept apart in a Petri-dish but sharing the headspace.</p> <p> </p>
Sample generalised Gross-Pitaevskii data for circulation statistics
<p>Sample dataset containing an instantaneous complex wave function field obtained from a three-dimensional generalised Gross-Pitaevskii simulation.</p> <p>The dataset is split into two files: one for the real part, and the other for the imaginary part of the wave function field <span class="math-tex">\(\psi(x, y, z)\)</span>.</p> <p>The dataset resolution is <span class="math-tex">\(256^3\)</span> grid points. The data is encoded as raw binary data, written in little-endian order, in double precision (64-bit floating point precision).</p>
openSAHE: Open Source Statistical Anatomical Atlas of the Human head for Electrophysiology Applications (precomputed atlases)
<p>Computed anatomical atlases of the human head at 100Hz, 1kHz 10kHz 100kHz and 1MHz. Electrical properties: resistivity, conductivity and relative permittivity in SI units. This dataset is part of the article 'Anatomical atlas of the upper part of the human head for electroencephalography and bioimpedance applications' by Moura, F, Beraldo R, Ferreira, L and Siltanen S, Physiological Measurement, Volume 42, Number 10, 2021. If you use any of these files, please add a reference to this <a href="https://iopscience.iop.org/article/10.1088/1361-6579/ac3218">article</a>.</p> <p>Source code available at https://github.com/fsmMLK/openSAHE</p>
A Bi-atrial Statistical Shape Model and 100 Volumetric Anatomical Models of the Atria
<p>This dataset is part of the publication "A bi-atrial statistical shape model for large-scale in silico studies of human atria: Model development and application to ECG simulations" by Nagel et al. (<a href="https://doi.org/10.1016/j.media.2021.102210">https://doi.org/10.1016/j.media.2021.102210</a>). It includes a bi-atrial statistical shape model built based on 47 MR and CT images (Left atrium segmentation challenge (Tobon-Gomez, 2015), Left atrium fibrosis and scar segmentation challenge (Karim, 2013), Left atrial wall thickness challenge (Karim, 2018)). ScalismoLab (https://scalismo.org) was used for parts of the model generation. Further Details are explained in the paper. The SSM is available as an h5 file including information about the mean shape's vertex locations and their triangulation as well as the eigenvectors and -values. </p> <p>100 random instances derived from the model are available. Each zip file contains the volumetric bi-atrial geometry as vtk file, which was augmented in a post-processing step with a homogeneous wall thickness, fiber orientation, intra-atrial bridges and material tags so that they are ready to use for electrophysiological simulations of atrial signals. Furthermore, the scalar field resulting from computing the gradient of the Laplace equation with the boundary conditions described by Piersanti et al. (Modeling cardiac muscle fibers in ventricular and atrial electrophysiology simulations, Computer Methods in Applied Mechanics and Engineering, 2020, <a href="https://doi.org/10.1016/j.cma.2020.113468">https://doi.org/10.1016/j.cma.2020.113468</a>) are available on the left and the right atrial instances. </p> <p>Furthermore, 95 geometries with uniformly distributed left atrial volumes are available in LAE_geometries.zip. </p>
Statistical analysis and dataset for: Invasive ant learning is not affected by seven potential neuroactive chemicals
<p>Linked to the journal article published in Current Zoology (<a href="https://doi.org/10.1093/cz/zoad001">https://doi.org/10.1093/cz/zoad001</a>).</p> <p><em><strong>Abstract</strong></em></p> <p>Argentine ants (<em>Linepithema humile</em>) are one of the most damaging invasive alien species worldwide. Enhancing or disrupting cognitive abilities, such as learning, has the potential to improve management efforts, for example by increasing preference for a bait, or improving ants’ ability to learn its characteristics or location. Nectar-feeding insects are often the victims of psychoactive manipulation, with plants lacing their nectar with secondary metabolites such as alkaloids and non-protein amino acids which often alter learning, foraging, or recruitment. However, the effect of neuroactive chemicals has seldomly been explored in ants. Here, we test the effects of seven potential neuroactive chemicals - two alkaloids: caffeine and nicotine; two biogenic amines: dopamine and octopamine, and three non-protein amino acids: β-alanine, GABA and taurine - on the cognitive abilities of invasive <em>L. humile</em> using bifurcation mazes. Our results confirm that these ants are strong associative learners, requiring as little as one experience to develop an association. However, we show no short-term effect of any of the chemicals tested on spatial learning, and in addition no effect of caffeine on short-term olfactory learning. This lack of effect is surprising, given the extensive reports of the tested chemicals affecting learning and foraging in bees. This mismatch could be due to the heavy bias towards bees in the literature, a positive result publication bias, or differences in methodology.</p>
A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy: Summary statistics - Health records
<p>Infectious agents contribute significantly to the global burden of diseases, through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 genome-wide association studies in 9,611 participants from UK Biobank, we identified NFKB1 as a locus associated with quantitative antibody responses to multiple pathogens including those from the herpes, retro- and polyoma-virus families. An insertion-deletion variant thought to affect NFKB1 expression (rs28362491), was mapped as the likely causal variant. This variant has persisted throughout hominid evolution and could play a key role in regulation of the immune response. Using 121 infection and inflammation related traits in 487,297 UK Biobank participants, we show that the deletion allele was associated with an increased risk of infection from diverse pathogens but had a protective effect against allergic disease. We propose that altered expression of NFKB1, as a result of the deletion, modulates haematopoietic pathways, and likely impacts cell survival, antibody production, and inflammation. Taken together, we show that disruptions to the tightly regulated immune processes may tip the balance between exacerbated immune responses and allergy, or increased risk of infection and impaired resolution of inflammation. </p> <p>-------------------------------------------------------------------------------------</p> <p>This dataset contains GWAS summary statistics for infection, inflammation, and allergy related traits in 487,297 individuals</p>
A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy: Summary statistics - Serology
<p>Infectious agents contribute significantly to the global burden of diseases, through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 genome-wide association studies in 9,611 participants from UK Biobank, we identified NFKB1 as a locus associated with quantitative antibody responses to multiple pathogens including those from the herpes, retro- and polyoma-virus families. An insertion-deletion variant thought to affect NFKB1 expression (rs28362491), was mapped as the likely causal variant. This variant has persisted throughout hominid evolution and could play a key role in regulation of the immune response. Using 121 infection and inflammation related traits in 487,297 UK Biobank participants, we show that the deletion allele was associated with an increased risk of infection from diverse pathogens but had a protective effect against allergic disease. We propose that altered expression of NFKB1, as a result of the deletion, modulates haematopoietic pathways, and likely impacts cell survival, antibody production, and inflammation. Taken together, we show that disruptions to the tightly regulated immune processes may tip the balance between exacerbated immune responses and allergy, or increased risk of infection and impaired resolution of inflammation. </p> <p>-------------------------------------------------------------------------------------</p> <p>This dataset contains GWAS summary statistics for quantitative antibody responses in 9611 individuals and results for a meta-analysis of UK Biobank and CoLaus/PsyCoLaus antibody responses.</p> <p> </p>
Codes to replicate statistical analysis in UPLIFT project Deliverable 2.4 Synthesis report, Chapter 6
<p>Policies attempting to mitigate the effects of urban inequality, often disregard affected citizens’ experiences, and thus fail to achieve maximum impact. By incorporating these perspectives into the policy design process, the project "Urban PoLicy Innovation to address inequality with and for Future generaTions" (UPLIFT), funded under the EU Horizon 2020 program aims to find innovative interventions in a bottom-up approach. The aims of UPLIFT project are to understand patterns and trends of inequality across Europe and to understand how individuals experience and adapt to inequality through participatory research. Moreover the project will together with the communities in four locations, co-design a policy tool aimed at addressing and reducing inequality and socio-economic divisions. The activity and results of the project can be followed at <a href="https://www.uplift-youth.eu/">https://www.uplift-youth.eu/</a>.</p> <p>Deliverable 2.4 (Synthesis report: socioeconomic inequalities in different urban contexts) is the final deliverable of work package 2 of the UPLIFT project, which aims to synthetize the main outcomes of the urban reports that described the policy environment around vulnerable individuals in the fields of education, employment and housing in 16 functional urban areas of the EU. In addition section 6.2 "Statistical analysis of linkages between economic development of cities, their public policy performance and inequality outcomes" of the report provides a statistical analysis of how local economic competitiveness and the local policy context affect urban deprivation and inequality among the young in European cities. The analysis is based on data from 2006, 2009, 2012, 2015 and 2019 of the Quality of Life in European Cities survey.</p>
Occupations on the map: Using a super learner algorithm to downscale labor statistics, data
<p>This repository contains all the input and output data (including maps) related to <a href="https://doi.org/10.1371/journal.pone.0278120">Van Dijk et al. (2022), Occupations on the map: Using a super learner algorithm to downscale labor statistics</a>. It does not contain several large (> 4GB) intermediate files, which summarize the results of the large number of machine learning models that were trained and tuned as part of the super learner algorithm. These files can be created by running the scripts in the supplementary GitHub repository: https://github.com/michielvandijk/occupations_on_the_map. All input and output maps produced as part of this study can also be accessed by means of an interactive web application: https://shiny.wur.nl/occupation-map-vnm.</p> <p>In this paper, we demonstrated an approach to create fine-scale gridded occupation maps by means of downscaling district-level labor statistics informed by remote sensing and other spatial information. We applied a super-learner algorithm that combined the results of different machine learning models to predict the shares of six major occupation categories and the labor force participation rate at a resolution of 30 arc seconds (~1x1 km) in Vietnam. The results were subsequently combined with gridded information on the working-age population to produce maps of the number of workers per occupation. The proposed approach can also be applied to produce maps of other (labor) statistics, which are only available at aggregated levels.</p>
Data to reproduce the results: Statistical power of spatial earthquake forecast tests
<p>We provide data needed to reproduce the figures from the publication titled "Statistical power of spatial earthquake forecast tests".</p>
zdravniki.sledilnik.org web page statistics
<p>The data uploaded here were used in a conference (MI'22) submission: Kaj se skriva v ozadju zdravniki.sledilnik.org created by the same authors.</p> <p>Data is automatically created by Google and Github actions. </p> <p>Github repositories linked to the project are:</p> <ul> <li><a href="https://github.com/sledilnik/zdravniki">sledilnik/zdravniki</a></li> <li><a href="https://github.com/sledilnik/zdravniki-data">sledilnik/zdravniki-data</a></li> </ul> <p>You can read more about the project on <a href="https://zdravniki.sledilnik.org/en/">zdravniki.sledilnik.org</a>.</p> <p>Authors would like to thank all of the <a href="https://covid-19.sledilnik.org/en/stats">COVID-19 tracker</a> project members for making this possible.</p>
Fine-mapped summary statistics for protein coding regions (i.e. cis regions) based on the Olink Explore 1536 and Explore Expansion technologies
<p>This data set contains fine-mapping results performed by SuSie for cis regions ±500kb around the protein coding gene) for protein targets as measured by the Olink Explore 1536 and Explore Expansion technologies in 1,180 individuals from EPIC Norfolk study (https://www.epic-norfolk.org.uk/). Only protein targets where fine-mapping predicted at least one credible set were included in the results. </p>
SUMMA/mizuRoute model configurations, parameters, and ensemble statistics for representative cryosphere basins
<p>Meteorological forcing is a major source of uncertainty in hydrological modeling. The recent development of probabilistic large-domain meteorological datasets enables convenient uncertainty characterization, which however is rarely explored in large-domain research. Tang et al. (2023) analyze how uncertainties in meteorological forcing data affect hydrological modeling in 289 representative cryosphere basins by forcing the Structure for Unifying Multiple Modeling Alternatives (SUMMA) and mizuRoute models with precipitation and air temperature ensembles from the Ensemble Meteorological Dataset for Planet Earth (EM-Earth). EM-Earth probabilistic estimates are used in ensemble simulation for uncertainty analysis. The results reveal the magnitude, spatial distribution, and scale effect of uncertainties in meteorological, snow, runoff, soil water, and energy variables.</p>
Accurate and Efficient Estimation of Local Heritability using Summary Statistics and LD Matrix -- Demo datasets for the HEELS tutorials
<p>We introduced a new estimator for local heritability, "HEELS", which attains comparable statistical efficiency as the REML estimator (such as those produced by GCTA and BOLT-REML) but only requires summary-level statistics – Z-scores from marginal association tests and the empirical LD. Our method has been implemented into an open-source Python-based command line tool. </p> <p>The datasets released here can be downloaded to test the two main functions of our software package: 1) estimating local heritability; 2) computing the low-dimensional representation of the LD matrix. They are meant to accompany the HEELS tutorials we have posted onto the wiki pages of our github repository: https://github.com/huilisabrina/HEELS/wiki.</p> <p> </p>
Summary statistics of stimulated fibroblast eQTLs
<p>This dataset comprises summary statistics from an eQTL mapping study of stimulated fibroblast eQTLs demonstrated in the manuscript entitled "Mapping interindividual dynamics of innate immune response at single-cell resolution" by Kumasaka et al.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.